Exploration of the microbiota in inflammatory diseases

Matthew Stoll MD

Research Computing Day September 13, 2012

We’re surrounded by bugs • Human body contains 100 trillion microbes

– Out-number human cells 10:1 • Human gut alone:

– ~ 99% of all of the microbiota – 3 pounds of bacteria

• 50% of fecal volume – ~ 1000 different species – 3 million different genes (100x human host)

Scher, Nat Rev Rheumatol 2011;7:569 De Cruz, Inflamm Bowel Dis 2012;18:372

Influences of microbiota composition

• Infant specific factors – Mode of delivery – Food source (breast vs bottle) – Maternal composition

• Diet • Geography • Antibiotic use

Palmer PLoS Biol 2007;5:e177

Delivery mode and neonatal flora

Domingues-Bello PNAS 2010;107:11971

Microbiota and diet / geography

De Filippo, PNAS 2010;107:14691

Burkina Faso (rural Africa)

Florence, Italy

Children age 1 – 6 years

These bacteria do stuff

Maccaferri Dig Dis 2011;29:525

Important metabolic functions

• Sugar / starches • Drug metabolism • Vitamin synthesis • Bile acid deconjugation

– Affects on triglycerides, cholesterol

Microflora appear to have a profound impact on a variety of

diseases

Immunology and gut bacteria

• Mice raised in GF conditions show: – Defective T, B, and innate cells in mucosal

lymphoid tissue – Smaller mucosal LNs – Fewer CD4 cells in peripheral LN – Th2 bias, with few Th17 cells – Decreased IgG and IgA levels

Mathis, Cell Host & Microbe 2011;10:297

Hygeine hypothesis

• Recent increases in – Inflammatory bowel disease – Atopy (allergies, asthma) – Type I diabetes

• Attributed to cleaner environments

Strachan, Jrnl Allergy Clin Immunol 1999;104:554

Germ-free humans, cont.

• Temporal: pre / post Industrial Revolution • IBD, atopy risk increase with income

– Across continents – Within countries

• Other markers of infectious burden – Day care attendance – Family size (increased # of sibs is protective)

Bach, Cell Immunol 2005;233:158 Blanchard, Am J Epidemiol 2001;154:328 Werner, Br Jrnl Dermatol 2002;147:95

Flora and animal models of disease

• Germ-free state results in altered / absent disease expression in several models of autoimmune diseases. – IBD – Spondyloarthritis with colitis – Rheumatoid arthritis – Type I Diabetes – Multiple sclerosis

Wu, Gut Microbes 2012;3:1

Disease transfer: TRUC model

• Colitis develops in double k/o mice: – RAG2 – T-bet (transcription factor)

• Role for flora evidenced by – Response to broad-spectrum abx – Absence of disease in progeny of abx-Tx mice – Development of colitis in wt mice housed with

TRUC mice

Garrett, Cell 2007;131:33

Microbiota and inflammatory diseases

• Inflammatory bowel disease (IBD) • Insulin-dependent (Type I) diabetes • Arthritis?

Microbiota and IBD: indirect evidence

• Altered flora in multiple studies • Decreased diversity

De Cruz, Inflamm Bowel Dis 2012;18:372 Comito, International Jrnl Inflam 2012;ePub

Diversity of flora in peds IBD

Papa, PLoS One 2012;7:e29242

Microbiota and IBD: therapeutic response to alterations in flora

• Antibiotics routinely used • Probiotics may be effective • Fecal microbiota transplantation

– Used extensively in chronic C. diff – Case reports in IBD

• Gnotobiotic facility at UAB can permit further study of microbiota transfer

Borody, Expert Rev Gastroenterol Hepatol 2011;5:653

Microbiota and Type I DM

• Diabetes Prediction and Prevention Study • Serial stool collections on high-risk infants • Case defined as pos. autoantibodies

– Ultimately dx with diabetes • Matched controls

Giongo, ISME 2011;5:82

Microbiota changes precede onset of Type I diabetes

Giongo, ISME 2011;5:82

Onset Onset

Increase in Bacteroides Decreased diversity

Juvenile arthritis: preliminary study

• Stool collected from – Three children with juvenile arthritis – One with psoriasis + joint pain – Two adult controls

• 16S sequencing performed

Kingdom

1 4 3 2 5 6

JIA JIA JIA Psor. Ctrl Ctrl

Phylum Verrucomicrobia

JIA JIA JIA Psor. Ctrl Ctrl

Family Verrucomicrobiaceae (Akkermansia muciniphila)

JIA JIA JIA Psor. Ctrl Ctrl

Start of a story…

• 6 yo female with psoriasis and joint pain • Subsequently developed abdominal pain

– Diagnosed with IBD • A. muciniphila chews up protective

mucin layer in intestines

Hmmm…..

Microbiota may impact non-inflammatory diseases

• Obesity • Metabolic syndrome

Obesity

• Differences in obese vs lean microbiome – Not universally detected

• Even if so, cause or effect? – Weight loss results in altered microbiome – Bacteria adapt to our diet

• Vegetarians enriched for bugs that can metabolize monosaccharides and disaccharides

Harris, Jrnl Obesity 2012;ePub Angelakis, Future Microbiol 2012;7:91

However, in mice… • Germ-free mice showed less weight gain on

Western diet

• Transplantation of microbiota from leptin-deficient mice resulted in increased body fat compared to recipients of microbiota from wt mice Turnbaugh, Nature 2006;444:1027

Backhed, PNAS 2007;104:979

And in humans… • Infant abx use is associated with increased

BMI during childhood1

• Infant microbiota is associated with future weight gain: – B fragilis correlates with BMI at age 32

– Low bidifobacter predicts overweight at age 73 • Upregulation in obese subjects of genes

involved in phosphotransferase, which is involved in putting sugars into cells4

1Trasande, Int Jrnl Obesity 2012;ePub 2Vael, Gut Pathogens 2011;3:8

3Kalliomaki, Am J Clin Nutr 2008;87:534 4Greenblum, PNAS 2012;109:594

Moreover… • 18 adults with metabolic syndrome

underwent small bowel lavage, with either: – Allogenic microbiota transfer (lean donors) – Autologous microbiota transfer

• Results – Increased microbial diversity – Increased insulin sensitivity – Weight changes not reported

Vrieze, Gastroenterol 2012; in press

Summary • New technology enables collection of

previously unattainable amounts of data • Analysis would not be possible without

high-power computing platforms discussed throughout today

• Areas of research include: – Ontogeny of microflora, factors that influence it – Effect of flora on inflammatory diseases – How to alter the flora to improve human health